Long-term population trends in urban birds in Europe and Czechia

Urbanization ranks among the most important processes induced by the human civilization that affects ecological communities at the same time. Birds are the most frequently studied organisms in relation to urbanization. Different birds' species show different abilities to adapt to urban areas, so urbanization works as an environmental filter. As urban environment undergoes extraordinarily high rate of change, the characteristics of the environmental filter are changing rapidly, too. This could influence populations of urban bird species. We can expect that the population change of the species will be related to the time since urbanization; specifically, the early urban colonizers will decline due to alteration of urban environment, while the recent urban colonizers will increase. I obtained data on population trends from 2000 to 2016 for 95 common urban bird species in 16 European countries. Thanks to the cooperation with local expert ornithologists, I collected the data about the time since urbanization of these species in respective countries and I related these two variables filtering out the influence of 9 other species-specific ecological characteristics. Bird population trends had a statistically significant relation to the time since urbanization: the species that became urbanized earlier...Urbanizace je jedním z nejdůležitějších procesů provázejících lidskou civilizaci a zároveň neodvratně účinkuje na ekologická společenstva. Nejlépe prozkoumanou skupinou organismů ve vztahu k urbanizaci jsou ptáci. Různé druhy ptáků mají odlišnou schopnost se na život ve městech adaptovat, takže pro ně urbanizace funguje jako určitý environmentální filtr. Města se přitom velmi dynamicky mění, a proto se může také upravovat charakteristika tohoto environmentálního filtru, což by se mohlo projevit ve změnách početnosti druhů žijících v městském prostředí. Lze předpokládat, že doba, po kterou druh ve městech žije, bude mít vztah k jeho populačním změnám, konkrétně že druhy, které města kolonizovaly dříve, v současnosti vlivem proměn městského prostředí ubývají, zatímco noví kolonizátoři přibývají. Získal jsem trendy 95 běžných urbanizovaných druhů ptáků od roku 2000 do roku 2016 v 16 evropských zemích. Za pomoci místních ornitologických expertů jsem získal údaje o době urbanizace každého z těchto druhů v každé zemi a za odfiltrování vlivu devíti dalších ekologických znaků jsem k sobě tyto dvě proměnné vztáhl. Populační trendy ptáků měly statisticky průkazný vztah k době urbanizace, přičemž druhy urbanizované dříve ubývaly, zatímco nedávno urbanizované druhy přibývaly. To může být zapříčiněno např. tím,...Department of EcologyKatedra ekologieFaculty of SciencePřírodovědecká fakult

Species traits and ecological conditions linked to bird colonisation of cities

Human settlements are a novel habitat type and species must respond to its ongoing expansion. For effective conservation of biodiversity, it is important to understand the mechanisms underlying these responses. This thesis focuses on urbanization in birds, from both the individual and community perspectives. The aim of this thesis is to find out if there are any "pre-adaptations" in some bird species to be successful city dwellers or if all birds can potentially exploit the urban environment when local conditions allow. According to the reviewed literature, I conclude that the urbanization in birds is not a universal pattern, but there are some specific traits shared by most of the urban birds. The successful urban species are mostly omnivorous or granivorous, they breed in trees or in cavities and, they are often ecological generalists. They are sometimes represented by non-native species occurring in the cities all over the world.Lidská sídla představují nový typ prostředí, na jehož rychlou expanzi musí organismy reagovat. Pro ochranu biodiverzity je klíčové pochopit, jaké mechanismy tuto reakci podmiňují. Tato práce se zaměřuje na urbanizaci u ptáků, a to jak z pohledu společenstva, tak z pohledu jednotlivce. Cílem práce je zjistit, zda jsou některé druhy "předurčeny" k úspěchu v městském prostředí, nebo zda do měst mohou potenciálně proniknout všechny druhy na základě lokálních podmínek. Rešerší dostupných literárních pramenů jsem zjistil, že nelze definovat univerzální mechanismus, kterým urbanizace ptáků probíhá, existují však společné vlastnosti, které sdílí většina ptáků obsazujících města. Úspěšné městské druhy jsou většinou omnivorní nebo granivorní, hnízdí na stromech nebo v dutinách a celkově jde spíše o ekologické generalisty. Velmi často jde o druhy nepůvodní, které se vyskytují ve městech po celém světě.Department of EcologyKatedra ekologiePřírodovědecká fakultaFaculty of Scienc

Non-extensivity of the configurational density distribution in the classical microcanonical ensemble

We show that the configurational probability distribution of a classical gas always belongs to the q-exponential family. Hence, the configurational subsystem is non-extensive in the sense of Tsallis. One of the consequences of this observation is that the thermodynamics of the configurational subsystem is uniquely determined up to a scaling function. As an example we consider a system of non-interacting harmonic oscillators. In this example, the scaling function can be determined from the requirement that in the limit of large systems the microcanonical temperature of the configurational subsystem should coincide with that of the canonical ensemble. The result suggests that Renyi's entropy function is the relevant one rather than that of Tsallis.Comment: 12 pages, no figure

Nuclear transport of single molecules: dwell times at the nuclear pore complex

The mechanism by which macromolecules are selectively translocated through the nuclear pore complex (NPC) is still essentially unresolved. Single molecule methods can provide unique information on topographic properties and kinetic processes of asynchronous supramolecular assemblies with excellent spatial and time resolution. Here, single-molecule far-field fluorescence microscopy was applied to the NPC of permeabilized cells. The nucleoporin Nup358 could be localized at a distance of 70 nm from POM121-GFP along the NPC axis. Binding sites of NTF2, the transport receptor of RanGDP, were observed in cytoplasmic filaments and central framework, but not nucleoplasmic filaments of the NPC. The dwell times of NTF2 and transportin 1 at their NPC binding sites were 5.8 ± 0.2 and 7.1 ± 0.2 ms, respectively. Notably, the dwell times of these receptors were reduced upon binding to a specific transport substrate, suggesting that translocation is accelerated for loaded receptor molecules. Together with the known transport rates, our data suggest that nucleocytoplasmic transport occurs via multiple parallel pathways within single NPCs

Valuing vicinity: Memory attention framework for context-based semantic segmentation in histopathology

The segmentation of histopathological whole slide images into tumourous and non-tumourous types of tissue is a challenging task that requires the consideration of both local and global spatial contexts to classify tumourous regions precisely. The identification of subtypes of tumour tissue complicates the issue as the sharpness of separation decreases and the pathologist’s reasoning is even more guided by spatial context. However, the identification of detailed tissue types is crucial for providing personalized cancer therapies. Due to the high resolution of whole slide images, existing semantic segmentation methods, restricted to isolated image sections, are incapable of processing context information beyond. To take a step towards better context comprehension, we propose a patch neighbour attention mechanism to query the neighbouring tissue context from a patch embedding memory bank and infuse context embeddings into bottleneck hidden feature maps. Our memory attention framework (MAF) mimics a pathologist’s annotation procedure — zooming out and considering surrounding tissue context. The framework can be integrated into any encoder–decoder segmentation method. We evaluate the MAF on two public breast cancer and liver cancer data sets and an internal kidney cancer data set using famous segmentation models (U-Net, DeeplabV3) and demonstrate the superiority over other context-integrating algorithms — achieving a substantial improvement of up to 17% on Dice score

Shut-down of type IX protein secretion alters the host immune response to Tannerella forsythia and Porphyromonas gingivalis

Tannerella forsythia and Porphyromonas gingivalis target distinct virulence factors bearing a structurally conserved C-terminal domain (CTD) to the type IX protein secretion system (T9SS). The T9SS comprises an outer membrane translocation complex which works in concert with a signal peptidase for CTD cleavage. Among prominent T9SS cargo linked to periodontal diseases are the TfsA and TfsB components of T. forsythia’s cell surface (S-) layer, the bacterium’s BspA surface antigen and a set of cysteine proteinases (gingipains) from P. gingivalis. To assess the overall role of the bacterial T9SS in the host response, human macrophages and human gingival fibroblasts were stimulated with T. forsythia and P. gingivalis wild-type bacteria and T9SS signal peptidase-deficient mutants defective in protein secretion, respectively. The immunostimulatory potential of these bacteria was compared by analyzing the mRNA expression levels of the pro-inflammatory mediators IL-6, IL-8, MCP-1 and TNF-$\alpha$ by qPCR and by measuring the production of the corresponding proteins by ELISA. Shot-gun proteomics analysis of T. forsythia and P. gingivalis outer membrane preparations confirmed that several CTD-bearing virulence factors which interact with the human immune system were depleted from the signal peptidase mutants, supportive of effective T9SS shut-down. Three and, more profoundly, 16 hours post stimulation, the T. forsythia T9SS mutant induced significantly less production of cytokines and the chemokine in human cells compared to the corresponding parent strain, while the opposite was observed for the P. gingivalis T9SS mutant. Our data indicate that T9SS shut-down translates into an altered inflammatory response in periodontal pathogens. Thus, the T9SS as a potential novel target for periodontal therapy needs further evaluation

Data Set Models and Exponential Families in Statistical Physics and Beyond

The exponential family of models is defined in a general setting, not relying on probability theory. Some results of information geometry are shown to remain valid. Exponential families both of classical and of quantum mechanical statistical physics fit into the new formalism. Other less obvious applications are predicted. For instance, quantum states can be modeled as points in a classical phase space and the resulting model belongs to the exponential family

Unifying generative and discriminative learning principles

<p>Abstract</p> <p>Background</p> <p>The recognition of functional binding sites in genomic DNA remains one of the fundamental challenges of genome research. During the last decades, a plethora of different and well-adapted models has been developed, but only little attention has been payed to the development of different and similarly well-adapted learning principles. Only recently it was noticed that discriminative learning principles can be superior over generative ones in diverse bioinformatics applications, too.</p> <p>Results</p> <p>Here, we propose a generalization of generative and discriminative learning principles containing the maximum likelihood, maximum a posteriori, maximum conditional likelihood, maximum supervised posterior, generative-discriminative trade-off, and penalized generative-discriminative trade-off learning principles as special cases, and we illustrate its efficacy for the recognition of vertebrate transcription factor binding sites.</p> <p>Conclusions</p> <p>We find that the proposed learning principle helps to improve the recognition of transcription factor binding sites, enabling better computational approaches for extracting as much information as possible from valuable wet-lab data. We make all implementations available in the open-source library Jstacs so that this learning principle can be easily applied to other classification problems in the field of genome and epigenome analysis.</p

Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis

<p>Abstract</p> <p>Background</p> <p>One of the challenges of bioinformatics remains the recognition of short signal sequences in genomic DNA such as donor or acceptor splice sites, splicing enhancers or silencers, translation initiation sites, transcription start sites, transcription factor binding sites, nucleosome binding sites, miRNA binding sites, or insulator binding sites. During the last decade, a wealth of algorithms for the recognition of such DNA sequences has been developed and compared with the goal of improving their performance and to deepen our understanding of the underlying cellular processes. Most of these algorithms are based on statistical models belonging to the family of Markov random fields such as position weight matrix models, weight array matrix models, Markov models of higher order, or moral Bayesian networks. While in many comparative studies different learning principles or different statistical models have been compared, the influence of choosing different prior distributions for the model parameters when using different learning principles has been overlooked, and possibly lead to questionable conclusions.</p> <p>Results</p> <p>With the goal of allowing direct comparisons of different learning principles for models from the family of Markov random fields based on the <it>same a-priori information</it>, we derive a generalization of the commonly-used product-Dirichlet prior. We find that the derived prior behaves like a Gaussian prior close to the maximum and like a Laplace prior in the far tails. In two case studies, we illustrate the utility of the derived prior for a direct comparison of different learning principles with different models for the recognition of binding sites of the transcription factor Sp1 and human donor splice sites.</p> <p>Conclusions</p> <p>We find that comparisons of different learning principles using the same a-priori information can lead to conclusions different from those of previous studies in which the effect resulting from different priors has been neglected. We implement the derived prior is implemented in the open-source library Jstacs to enable an easy application to comparative studies of different learning principles in the field of sequence analysis.</p